'\" t
.TH samtools-targetcut 1 "2 September 2022" "samtools-1.16.1" "Bioinformatics tools"
.SH NAME
samtools targetcut \- cut fosmid regions (for fosmid pool only)
.\"
.\" Copyright (C) 2008-2011, 2013-2018 Genome Research Ltd.
.\" Portions copyright (C) 2010, 2011 Broad Institute.
.\"
.\" Author: Heng Li <lh3@sanger.ac.uk>
.\" Author: Joshua C. Randall <jcrandall@alum.mit.edu>
.\"
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.
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.SH SYNOPSIS
.PP
samtools targetcut
.RB [ -Q
.IR minBaseQ ]
.RB [ -i
.IR inPenalty ]
.RB [ -0
.IR em0 ]
.RB [ -1
.IR em1 ]
.RB [ -2
.IR em2 ]
.RB [ -f
.IR ref "] " in.bam

.SH DESCRIPTION
.PP
This command identifies target regions by examining the continuity of read depth, computes
haploid consensus sequences of targets and outputs a SAM with each sequence corresponding
to a target. When option
.B -f
is in use, BAQ will be applied. This command is
.B only
designed for cutting fosmid clones from fosmid pool sequencing [Ref. Kitzman et al. (2010)].

.SH OPTIONS
.TP 8
.BI -Q \ minBaseQ
Ignore bases with quality less than \fIminBaseQ\fR.

.TP
.BI -i \ inPenalty
Penalty for in state transition.
.TP
.BI -0 \ em0
Emission score 0.
.TP
.BI -1 \ em1
Emission score 1.
.TP
.BI -2 \ em2
Emission score 2.
.TP
.BI -f\  ref
Reference FASTA file.

.SH AUTHOR
.PP
Written by Heng Li from the Sanger Institute.

.SH SEE ALSO
.IR samtools (1)
.PP
Samtools website: <http://www.htslib.org/>
